
#include "../pdb_index/aa_table.h"

/**

   \defgroup Substitution Substitution matrices

   Transforms substitution matrix weights into a metric.  Currently,
   this simply linearly scales the elements of the matrices so that
   favorable substitutions receive low distances, and all distances
   are >= 0.

   Currently, the only substitution matrix available is blosum62,
   although adding more would be relatively simple.

   \ingroup Metric
*/
double substitution_matrix_distance (unsigned char a, unsigned char b);

